--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BlibBuild.xml	Tue May 08 14:16:45 2018 -0400
@@ -0,0 +1,107 @@
+<tool id="BlibBuild" name="BlibBuild" version="@VERSION@.0">
+    <description>create a library of peptide MS/MS spectra</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ## Need to symlink to data using name with extension that recognizes 
+        #import re
+        #set $exts = {'mgf':'MGF', 'mzml':'mzML', 'mzxml':'mzXML', 'ms2': 'ms2', 'wiff':'wiff'}
+        #for $pl in $peak_lists:
+            #set $dt = $pl.extension
+            #set $bn = $pl.display_name.split('/')[-1]
+            #set $ext = $exts[$dt.lower()]
+            #set $input_name = $re.sub(str(r'(?i)[.]' + $dt),str('.' + $ext), str($bn))
+            ln -s -f '${pl}' '${input_name}' &&
+            #set $encoded_id = $__app__.security.encode_id($pl.id)
+            echo "Spectrum:${pl.display_name}(API:${encoded_id}) " &&
+        #end for
+        #set $ext = $identification.extension
+        #set $ident = $identification.display_name.split('/')[-1].replace('.' + str($identification.extension), "") + "." + $ext
+        ln -s -f '$identification' '$ident' &&
+        #if $existing_blib:
+            cp '$existing_blib' spectra.blib &&
+        #end if
+        BlibBuild 
+        #if str($cutoff): 
+            -c $cutoff
+        #end if
+        #if $authority: 
+            -a $authority
+        #end if
+        #if $library_id: 
+            -i $library_id
+        #end if
+        '$ident' spectra.blib
+        && cp spectra.blib $blib
+        #if $convert_to_ms2:
+            && BlibToMs2 -f '$ms2' spectra.blib
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="identification" type="data" format="mzid" label="Peptide Identification Results" >
+            <help>
+            </help>
+        </param>
+        <param name="peak_lists" type="data" format="mzml,mzxml,mgf" multiple="true" optional="true" 
+            label="Spectrum Datasets used in the peptide identification"/>
+        <param name="existing_blib" type="data" format="sqlite" label="Add to existing Blib" optional="true"/>
+        <param name="cutoff" type="float" value="" min="0.0" max="1.0" optional="true" 
+            label="Specify the cutoff score (0-1)" 
+            help=" below which peptide-spectrum matches will be excluded from the library."/>
+        <param name="authority" type="text" value="" optional="true" label="LSID authority. Default proteome.gs.washington.edu"/>
+        <param name="library_id" type="text" value="" optional="true" label="LSID library ID. Default uses file name"/>
+        <param name="convert_to_ms2" type="boolean" truevalue="yes" falsevalue="no" label="Output a MS2"/>
+    </inputs>
+    <outputs>
+        <data name="blib" format="sqlite" label="Blib from ${on_string}" from_work_dir="spectra.blib" />
+        <data name="ms2" format="ms2" label="MS2 from ${on_string}" from_work_dir="spectra.ms2" >
+            <filter>convert_to_ms2 == True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="identification" ftype="mzid" value="msgf-test.mzid"/>
+            <param name="peak_lists" ftype="mzml" value="msgf-test.mzML"/>
+            <param name="convert_to_ms2" value="True"/>
+            <output name="ms2">
+                <assert_contents>
+                    <has_text_matching expression="D\tseq\tFKWNGTDTNSAAEK" />
+                    <has_text_matching expression="D\tmodified seq\tFKWNGTDTNSAAEK" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
+
+BlibBuild_ creates a library of peptide MS/MS spectra from a variety of different database search results. 
+
+::
+
+  Usage: BlibBuild [options] <*.blib|*.pep.xml|*.pep.XML|*.pepXML|*.sqt|*.perc.xml|*.dat|*.xtan.xml|*.idpXML|*.group.xml|*.pride.xml|*.msf|*.pdResult|*.mzid|*msms.txt|*final_fragment.csv|*.proxl.xml|*.ssl|*.mlb|*.tsv|*.osw>+ <library_name>
+   -o                Overwrite existing library. Default append.
+   -S  <filename>    Read from file as though it were stdin.
+   -s                Result file names from stdin. e.g. ls *sqt | BlibBuild -s new.blib.
+   -u                Ignore peptides except those with the unmodified sequences from stdin.
+   -U                Ignore peptides except those with the modified sequences from stdin.
+   -H                Use more than one decimal place when describing mass modifications.
+   -C  <file size>   Minimum file size required to use caching for .dat files.  Specifiy units as B,K,G or M.  Default 800M.
+   -c <cutoff>       Score threshold (0-1) for PSMs to be included in library. Higher threshold is more exclusive.
+   -v  <level>       Level of output to stderr (silent, error, status, warn).  Default status.
+   -L                Write status and warning messages to log file.
+   -m <size>         SQLite memory cache size in Megs. Default 250M.
+   -l <level>        ZLib compression level (0-?). Default 3.
+   -i <library_id>   LSID library ID. Default uses file name.
+   -a <authority>    LSID authority. Default proteome.gs.washington.edu.
+   -x <filename>     Specify the path of XML modifications file for parsing MaxQuant files.
+   -P <float>        Specify pusher interval for Waters final_fragment.csv files.
+   -d [<filename>]   Document the .blib format by writing SQLite commands to a file, or stdout if no filename is given.
+
+
+.. _BlibBuild: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild
+.. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
+    ]]></help>
+    <expand macro="citations" />
+</tool>